Tag Archives: research

A protein being termed ‘Ovulation-inducing Factor’ has been found in the seminal fluid of a variety of male mammals, which stimulates the female brain to produce eggs (the process of which is called ovulation).

Ovulation-Inducing Factor

The presence of such a protein was first discovered when female camels ovulated soon after injection with semen. This experiment was repeated with llamas and alpacas to see the same results. However, the species in which it was first discovered (rabbits and koalas, besides camels) are called ‘induced ovulators’, meaning that the females produce eggs only upon insemination by the male. In other mammals including horses, pigs and humans, ovulation is spontaneous—meaning that there is a biological cycle in the female which leads to a buildup of hormones leading to the release of the egg. It turned out that OIF was also present in the semen of these spontaneous ovulators. Did OIF actually change ovulation rhythms in them?

It isn’t just sperm that is present in semen. A protein called NGF might stimulate production of eggs for the sperm to fuse with. [Image Credit: biology.ucsd.edu]

The conservation of this protein must have a biological significance, and one way to determine that was to characterize the protein OIF. Researchers isolated this protein from llamas and bulls and tried to identify it in order to determine how its mechanism of action in the female body. By comparing protein structures, they found that this protein is actually a Nerve Growth Factor (NGF), a protein commonly found in nerve cells of the body. To confirm this finding, they isolated NGF from mice and injected it into llamas, and found that ovulation was induced in the llamas.

NGF Acts as a Hormone on the Female Brain

The NGF protein can act on the hypothalamus of the female brain via a system of hormones. What this means is that a substance that is a part of the male body can interfere with the female’s reproductive cycle. Is this true in humans too? We don’t know, but it might mean that we can rely less on birth control methods relying on abstinence during some days of the menstrual cycle. We know that human semen contains NGF, and that NGF can act on female hormones, but the female reproductive cycle is one that is tightly controlled, and further studies will have to be performed to determine the extent to which OIF/NGF can influence ovulation in spontaneous ovulators. In cows, injection of OIF has shown to alter ovarian function and shortens the ovarian cycles of cows.

“The idea that a substance in mammalian semen has a direct effect on the female brain is a new one,” says Gregg Adams, who headed the research team. “This latest finding broadens our understanding of the mechanisms that regulate ovulation and raises some intriguing questions about fertility.” Perhaps a host of fertility-related issues could be traced back to deficiencies in NGF in male semen, or NGF receptors in females.

In a couple of decades from now, your version of the Bible or Harry Potter (or the best-selling book of the 22nd century, whatever that might be) might just be stored in a small vial of liquid or on small chips. Harvard University researchers have just encoded a book in DNA fragments instead of on physical copy or e-copy.

The Alphabets of DNA

DNA is made up of building blocks called nucleotides, similar to how the English alphabet is made up of building blocks called alphabets. In the language of DNA, there are just 4 alphabets instead of 26, ‘A’, ‘T’, ‘G’ and ‘C’. Moving to information theory, each letter in DNA can thus encode 2 bits of information. Each nucleotide weighs around 250 Dalton (each Dalton weighs 1.66×10-24g). Thus, a single gram of single-stranded DNA could encode 455 exabytes (1 exabyte is 1018 bytes) of information. The previous sentence says ‘single-stranded’ because in nature, DNA molecules form two strands that wrap around each other to form a helix. Even keeping in mind this condition, a single gram of double stranded DNA could still encode around 225 exabytes, not a small number!

The four building blocks of DNA, also called bases (shown in green, red, yellow and blue) can be used as effective storage devices. [Image Credit: restlessmindboosters]

Translating English into DNAese

Encoding a book in DNA essentially means translating English into a code in a language of 4 letters. An html-encoded book called ‘Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves’ containing 53,426 words, 11 JPG images and a Javascript program has not been translated into the language of DNA. While DNA-encoding has been done on smaller scales before, the increasing ease and decreasing cost of DNA sequencing has made it possible to encode larger quantities of text in this biological molecule.

The entire book was translated onto small fragments of DNA called oligonucleotides. Each of these fragments had information from the book, and a small block with information for the ‘address’, where in the book the block belonged to. Thus, a ‘library’ of oligonucleotides is created on a DNA microchip. To ‘read’ the book, this library has to be amplified and sequenced using molecular approaches. These researchers encoded just one bit of information per DNA base instead of the maximum two, made multiple copies of the same oligonucleotide fragment so that errors could be accounted for, and still obtained a whopping density of 5.5 petabits (1015 bits) per millimeter cube.

Current costs of sequencing make this technology prohibitive. However, the costs of DNA synthesis and sequencing are decreasing exponentially every year, making this a feasible storage molecule for the future. DNA is also stable at room temperature meaning it can be preserved for long periods. While DNA storage and retrieval is slower compared to other methods, its scale offers huge potential. It could thus be used in applications involving archival storage of massive amounts of data.

Lasers have been around for a long time now. They are so ubiquitous, you can find them in computers, hunting rifle scopes, medical devices, and even a child’s play thing. Believe it or not, about 50 years ago, most of the devices that use lasers had not even been conceived of. What you also may not know is that the laser has an older cousin that has been sitting quietly on the shelf for nearly 50 years. It’s name is MASER.

Where LASER is an acronym for Light Amplification by Stimulated Emission of Radiation, MASER is Microwave Amplification by Stimulated Emission of Radiation. So basically, instead of visible light, the MASER produces a concentrated beam of microwaves. Though MASERs were actually developed first, the conditions it took to create them were very difficult to achieve. For instance, they required nearly absolute zero temperatures to operate. New research done by Britain’s National Physics Laboratory (NPL) and Imperial College, London has resulted in a solid-state room temperature MASER. The research has been published in the journal Natureand was led by Dr. Mark Oxborrow.

The MASER core via NPL Youtube Video

Up until now, MASERS were only a thing of physics labs and research facilities. The only real practical use for them was in atomic clocks. Now that the NPL scientists have been able to remove the extreme environmental conditions from the MASER, more practical applications are likely to be introduced. According to an NPL press release, “MASERs could be used to make more sensitive medical instruments for scanning patients, improved chemical sensors for remotely detecting explosives; lower-noise read-out mechanisms for quantum computers and better radio telescopes for potentially detecting life on other planets.” In the embedded video below, Dr. Oxborrow gives a brief description of the MASER and shows the core they invented to make all of this possible.

Conventional MASERs work by directing microwaves at crystals such as ruby. Unfortunately, this material requires extremely low temperatures, as well as a lot of costly magnets to work. The NPL scientists discovered a new type of crystal called p-terphenyl crystal. This crystal is “doped” pentacene which allows it to be used to amplify microwaves at room temperature. There are still challenges facing the MASER. One, is to get it to work continuously instead of in pulses. The other, is to get it to operate in a broader range of microwave frequencies to make it more useful. To keep up with the MASER research, visit http://www.npl.co.uk/news/maser.

Our body comes with an inbuilt drainage system called the lymphatic system. The tissues in our body lie in a pool of fluid called the interstitial fluid. While most of this fluid is directly circulated and recirculated from and into the blood vessels (called the body’s circulatory system), about 1% of this fluid is re-circulated through a different route. Interstitial fluid enters a network of vessels called lymph vessels, which in turn drain excess proteins and waste material from this fluid and into larger blood vessels for recirculation or destruction. The lymphatic system is thus an accessory system that acts in parallel with the blood circulatory system to remove excess proteins and solutes from tissues.

Fluid Flow in the Brain

Apart from blood vessels, the brain also has a fluid called the cerebrospinal fluid (CSF) circulating in its outer parts. This fluid maintains brain pressure and protects the brain from physical injury. However, a system analogous to the body’s lymphatic system has not been seen in the brain till date. This is surprising because the brain has a very high metabolic rate and brain cells are particularly sensitive to the balance of chemicals in their environment. So how does brain tissue drain waste? It has been speculated that the CSF could perform the drainage role in the brain.

Injecting Fluorescent Molecules into the Brain

How does waste from the brain tissue get out of the brain? If it is through the CSF, then the question becomes—how do tissues release their waste into the CSF which has so far been found only in the sub-arachnoid space, the outer areas of the brain? Researchers from the University of Rochester injected small amounts of fluorescent ‘tracer ‘molecules into the brain’s CSF, and as the name suggests, traced the destinations of these tracers by brain scans. They found new channels through which the CSF flows, right into the brain tissue, called brain parenchyma. They could trace the paths of these molecules, and using molecules of different sizes, they could estimate the volumes of these paths through the brain.

The thick vessel is an artery in the brain of a mouse. In green is cerebrospinal fluid in a channel along the outside of the artery. [Image Credit: University of Rochester medical Center]They found that the CSF traverses the inner parts of the brain including the space around brain tissue in hitherto unknown channels that lie parallel to and on the boundaries of the brain’s arteries and veins, formed by cells called astrocytes. Moreover, when a water-transport gene called AQP4 was deleted in mice, fluid flow through this system was suppressed, meaning that water-transport helps build up the pressure to move things along in this system using bulk-flow or convection. The water-pressure creates a pressure allowing waste to be drained away faster. The brain’s lymphatic system has thus been found, and is being referred to as the ‘glymphatic system’, called so because cells called glial cells help create pressure.

Alzheimer’s Molecule Takes This Route

The researchers went one step further and traced the path of fluorescent-tagged amyloid b, the protein responsible for Alzheimer’s disease. They found that this protein travels along this route of ‘glymphatic’ blood vessels. This insight provides therapeutic possibilities. Improving flow through this system could speed up clearance of neurodegradative molecules like amyloid-beta from the brain. Conversely, impeding or reducing flow through this system might help retain vaccines or drugs in the brain tissue for a longer period of time. If these vessels are also routes for migrating cells, could the metastasis of cancerous tumour cells be dependent on this system too?

“Waste clearance is of central importance to every organ, and there have been long-standing questions about how the brain gets rid of its waste,” said Maiken Nedergaard, M.D., D.M.Sc., lead author of the paper and co-director at the University of Rochester’s Center for Translational Neuromedicine. “This work shows that the brain is cleansing itself in a more organized way and on a much larger scale than has been realized previously.You can read about this research here and here.

A record breaking Burmese python has been found in the Florida everglades. The snake was a record breaking 17-foot-7-inches long and weighed 164.5 pounds. It was also full of eggs which numbered 87, another record breaker.

Gigantic Burmese python being examined by researchers at the Florida Museum of Natural History (University of Florida photo by Kristen Grace/Florida Museum of Natural History)

The snake has been handed over to the Florida Museum of Natural History by officials from Everglades National Park. Burmese pythons are native to southeast Asia, but have become quite an invasive species in the Florida everglades as many people tried to keep them as pets. Once the pet owners realize how large these guys can get, they often release them into the wild. Unfortunately, due to the size of this particular find, it is becoming apparent that they are thriving in their new home. “This thing is monstrous, it’s about a foot wide,” said Florida Museum herpetology collection manager Kenneth Krysko. “It means these snakes are surviving a long time in the wild, there’s nothing stopping them and the native wildlife are in trouble.”

Skip Snow, a park wildlife biologist, said, “I think one of the important facts about this animal is its reproductive capability…There are not many records of how many eggs a large female snake carries in the wild. This shows they’re a really reproductive animal, which aids in their invasiveness.”

The researchers hope they can examine this specimen to find out what its eating habits are and hopefully discover some way they can curtail the spread of this deadly invasive species. As it stands now, the Burmese python has no known predators and one this size can eat just about anything it wants.

A movie called ‘Ratatouille’ showed us a cartoon mouse that could cook up wonders. The real world matches this with mice that don’t just squeak, but sing too.

Singing for the Women

Scotinomys teguina are mice from the mountains of Costa Rica which communicate by singing. Before you start preparing to teach your next non-avian pet the latest from Adele, the singing capacity of these marvelous creatures is restricted to trilling—a rapid alternation between two adjacent notes. In several species of birds, males with greater trill production are seen to be greater threats by rivals, and seen as more attractive by females. Likewise, the male singing mouse emits a series of rapid high-pitched chirps to attract mates and fend off rivals.

Researchers at the University of Texas are now studying these mice to try and understand the genes that lead to this singing behavior—genes which could in turn regulate language in humans. It is known that music and language are processed by the same brain systems in humans in a part of the brain called the temporal lobes.

Looking for a ‘Singing Gene’

It is one gene in particular that is being studied, a gene called FOXP2 (Forkhead Box Protein P2). This gene is highly conserved across humans, singing mice and lab mice. In humans, mutations of this gene has been found to lead to speech and language disorders. In birds, removing this gene leads to inaccurate song imitation. The research team is sequencing this entire gene in the singing mice and looking for segments of DNA that are present only in the singing mouse as opposed to the lab mouse; from this set of changes, the team then filters out those that are likely to have occurred by chance and have no biological significance. The remaining gene changes are those that could be responsible for the ability of the singing mice to trill.

Another way to study this single gene is to look at its function. This protein regulates the expression and activities of a host of other proteins—what are they? “We found that when an animal hears a song from the same species, these neurons that carry FOXP2 become activated. So we think that FOXP2 may play a role in integrating that information,” said Lauren O’Connell, a researcher in Steven Phelps’s lab, where this research is being conducted. They are now making the mice listen to songs, and record all the genes that are activated, to see which ones could be activated by FOXP2. This information will help us form the complete link between the gene and the biological property of singing or language in humans.

Recently, I shared an article with you called “Diseased Trees are Potential Source for Greenhouse Gas“. You may want to take a moment and familiarize yourself with the original article before going any further. In a nutshell, the article laid out some interesting new research by Yale Ph.D. candidate Kristofer Covey. His research centered around the amount of methane gas, well known for its contribution to the greenhouse affect, that trees were putting out. His research found that trees that were diseased with a common fungus had conditions favorable to the production of greenhouse gases. Most of the trees were pretty old between 80-100 years old.

The reason I am updating this article is because I was able to get in contact with Kris and found out a couple pieces of information that I thought might be worth sharing with you the reader. I had two questions for Kris and he was kind enough to respond. Below, you can see the questions I asked with his answer following.

Question #1. – I am curious how you or the authors feel this affects the global warming debate?

I think the most important thing here is that although it appears as though trees may be producing and releasing significant amounts of methane, they still offer significant climate benefit. Our results indicate that in the stands studied the methane being released is equivalent in it’s climate warming effect to 18% of the carbon sequestered annually. If, as we suspect, this phenomenon is widespread then there would be implications for carbon markets and other programs that make use of forests as a mitigation tool in climate change action.

Question #2. – What potential remedies could be put in place to eliminate the source of this fungal activity?

While there aren’t practical ways to limit fungal infection in forest trees (these fungi are normal and essentially ubiquitous agents); however, we did find species level differences (red maple seems to produce far more than the other species studied ex.) indicating that there may management strategies that could optimize the tradeoff between carbon sequestration and methane production. That said, there’s a great deal of questions to ask before specific recommendations could be made. We are only now recognizing this pathway exists!

I thought it was important to share this information because it clears up some concern that trees aren’t destroying our atmosphere. Basically, even the diseased trees still clean up bad carbon but just not as much as a healthy one could.

Fossil Questions if Our Ancestors Had Cousins

There exists a fossil of a human skull, labelled 1470, which has been at the center of quite a bit of controversy since its discovery in 1972. This fossil, said to be from 2 million years ago, was different enough from the existing human ancestor at that period—Homo erectus—for some scientists to propose that it belonged to a new species. And thus were formed two warring camps. One said that 1470 belonged to Homo erectus, and the difference could be accounted for by variation within a species. The other camp believed that 1470 represented a remnant of a new species that might have existed along with Homo erectus, meaning that the lineage of current humans might not be as linear as we think it is.

A timeline in Homo sapiens evolution. Homo rudolfensis is the contested species which might have co-existed with two others. [Image Credit: Nature]
Now, the discovery of three new fossils has strengthened the claims of the second camp. These were discovered by a team led by Meave Leakey (who was also involved in discovering 1470) also near Lake Turkana in Kenya. The new fossils, which are from 1.78 to .95 million years ago, resemble fossil 1470 in skull structure by having similarly large and flat faces. Scientists are saying that the presence of more than a single outlier suggests that 1470 wasn’t just an unusual case in the species Homo erectus, but just one among a number of individuals in an altogether new species, which they are calling Homo rudolfensis. This finding contradicts the belief that our species evolved from the ancestors we share with apes in a strictly linear progression. The authors of this research believe that 3 species existed simultaneously—erectus, 1470 and a third branch— of which erectus eventually evolved to become Homo sapiens.

Not Definitive Evidence

This discovery isn’t convincing the critics, though, who think the evidence is not definite, and that the three fossils could still be diverse members of the same species. For now, our family tree remains murky.

Just when you thought the global warming debate or (depending on the mood that week) climate change debate, couldn’t get any more complicated, new research suggests that trees may be a significant source of the greenhouse gas, methane. That’s right folks, I said trees. You know, those things we plant in droves every Earth Day while singing some happy tune about saving the environment and making the world a better place to breathe. I really don’t mean to sound snarky here, but the poor global warming debate is already hopelessly mired in political rhetoric as it is. Now, we have to contend with research suggesting that trees may be a significant contributor of methane, which is a greenhouse gas.

Now, before you go get the chainsaws and start deforesting the neighborhood, let’s put this new study in context. Researchers at the Yale School of Forestry and Environmental Studies examined 60 trees at Yale Myers Forest in northeastern Connecticut. They tested for concentrations of methane and found that these particular trees had concentrations 80,000 times ambient levels. It is important to note that the trees themselves weren’t the culprit rather, it was a fungus that was eating them from the inside out. This resulted in favorable conditions for methane producing microorganisms called methanogens. Most of these trees were between 80-100 years old and were diseased. Red maples showed the highest concentrations of methane but other significant contributors were oak, birch and pine. Methane levels were also more than 3 times higher during the summer which suggests that summer heat and higher methane output could create a spiral of elevating temperatures.

According to a Yale press release, “These are flammable concentrations,” said Kristofer Covey, the study’s lead author and a Ph.D. candidate at Yale. “Because the conditions thought to be driving this process are common throughout the world’s forests, we believe we have found a globally significant new source of this potent greenhouse gas.” “No one until now has linked the idea that fungal rot of timber trees, a production problem in commercial forestry, might also present a problem for greenhouse gas and climate change mitigation,” said Mark Bradford, a co-author and Assistant Professor of Terrestrial Ecosystem Ecology at F&ES.

This is groundbreaking research because no previous studies have made the correlation between fungal timber rot and increased green house emissions. These findings present a new target for scientists interested in climate change and the potential that aging forests may have on greenhouse gasses. This study was published in Geophysical Research Letters.

It’s not just our bodies that have left-handedness and right-handedness. It has long been known that molecules within living organisms also possess the property of asymmetry, also called chirality. This simply means that a molecule does not match its mirror image. Thus, while the proteins in our body are composed of amino acids that are left-handed, the sugars are right-handed.

The Importance of Handedness in Life

This preponderance in one type of handedness has long been considered as essential property and prerequisite of ‘life’ itself. This is mainly because inorganic substances contain roughly equal quantities of both left-handed and right-handed molecules. Thus the question of why only molecules with one type of ‘handedness’ would arise in living organisms from a nearly equal distribution of molecules continues to be important in studying the origins of life.

This intrinsic asymmetry is actually being used by space missions, like the ExoMars mission, as an elegant way of detecting traces of life in outer space.

The Tagish Lake Meteorite, which showed an excess of ‘L’ aspartic acid, an amino acid. [Image Credit: wikipedia]Meteorites found at Taglish lake in Canada, have however shown results that bring this hypothesis to a screeching halt. Researchers have analysed these meteorites for proportions of left- handed ‘L’ and right-handed ‘R’ amino acids, and found an excess of ‘L’ types for some of them.

Meteors as Remnants of a Pre-Life Universe

Meteors represent parts of the extra-terrestrial universe before the emergence of life. Amino acids in these meteors were confirmed to be extra-terrestrial in origin by studying their carbon isotopes. Researchers are proposing that heating in the early days of the solar system melted ice to produce water which dissolved existing amino acids into populations of chiral asymmetric molecules. The amino acids which were found to be excessively present in one form are susceptible to forming asymmetric populations depending on the chirality of the starting amino acid. Thus, a small quantity of an asymmetric molecule could have set off a cascade leading to a highly asymmetric group of amino acids.

“As evidence mounts that [left-handed] excess occurs naturally across bodies in the solar system, any strategies designed to search for life based on looking for this excess require serious rethinking,” saysAlberto Fairen of the SETI Institute in Mountain View, California.

This does NOT, however, in any way, disprove the existence of extraterrestrial life. Chirality is just one aspect of life, and the search of life in outer space will continue.